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JSS
JSS

Journal of Statistical Software

November 2012, Volume 51, Issue 7.

spacetime: Spatio-Temporal Data in R

JSS Journal of Statistical Software November 2012, Volume 51, Issue 7. <a href=http://www.jstatsoft.org/ spacetime : Spatio-Temporal Data in R ifgi Institute Univ er sity for of Geoinformatics Müns t e r Edzer Pebesma Abstract This document describes classes and methods designed to deal with different types of spatio-temporal data in R implemented in the R package spacetime , and provides exam- ples for analyzing them. It builds upon the classes and methods for spatial data from package sp , and for time series data from package xts . The goal is to cover a number of useful representations for spatio-temporal sensor data, and results from predicting (spa- tial and/or temporal interpolation or smoothing), aggregating, or subsetting them, and to represent trajectories. The goals of this paper are to explore how spatio-temporal data can be sensibly represented in classes, and to find out which analysis and visualisation methods are useful and feasible. We discuss the time series convention of representing time intervals by their starting time only. This vignette is the main reference for the R package spacetime ; it been published as Pebesma ( 2012 ), but is kept up-to-date with the software. Keywords :˜Time series analysis, spatial data, spatio-temporal statistics, Geographic Informa- tion Systems. 1. Introduction Spatio-temporal data are abundant, and easily obtained. Examples are satellite images of parts of the earth, temperature readings for a number of nearby stations, election results for voting districts and a number of consecutive elections, trajectories for people or animals possibly with additional sensor readings, disease outbreaks or volcano eruptions. Schabenberger and Gotway ( 2004 ) argue that analysis of spatio-temporal data often happens conditionally , meaning that either first the spatial aspect is analysed, after which the temporal aspects are analysed, or reversed, but not in a joint, integral modelling approach, where space and time are not separated. As a possible reason they mention the lack of good software, " id="pdf-obj-0-16" src="pdf-obj-0-16.jpg">

ifgi

Institute University for of Geoinformatics Münster

JSS Journal of Statistical Software November 2012, Volume 51, Issue 7. <a href=http://www.jstatsoft.org/ spacetime : Spatio-Temporal Data in R ifgi Institute Univ er sity for of Geoinformatics Müns t e r Edzer Pebesma Abstract This document describes classes and methods designed to deal with different types of spatio-temporal data in R implemented in the R package spacetime , and provides exam- ples for analyzing them. It builds upon the classes and methods for spatial data from package sp , and for time series data from package xts . The goal is to cover a number of useful representations for spatio-temporal sensor data, and results from predicting (spa- tial and/or temporal interpolation or smoothing), aggregating, or subsetting them, and to represent trajectories. The goals of this paper are to explore how spatio-temporal data can be sensibly represented in classes, and to find out which analysis and visualisation methods are useful and feasible. We discuss the time series convention of representing time intervals by their starting time only. This vignette is the main reference for the R package spacetime ; it been published as Pebesma ( 2012 ), but is kept up-to-date with the software. Keywords :˜Time series analysis, spatial data, spatio-temporal statistics, Geographic Informa- tion Systems. 1. Introduction Spatio-temporal data are abundant, and easily obtained. Examples are satellite images of parts of the earth, temperature readings for a number of nearby stations, election results for voting districts and a number of consecutive elections, trajectories for people or animals possibly with additional sensor readings, disease outbreaks or volcano eruptions. Schabenberger and Gotway ( 2004 ) argue that analysis of spatio-temporal data often happens conditionally , meaning that either first the spatial aspect is analysed, after which the temporal aspects are analysed, or reversed, but not in a joint, integral modelling approach, where space and time are not separated. As a possible reason they mention the lack of good software, " id="pdf-obj-0-32" src="pdf-obj-0-32.jpg">

Edzer Pebesma

Abstract

This document describes classes and methods designed to deal with different types of spatio-temporal data in R implemented in the R package spacetime, and provides exam- ples for analyzing them. It builds upon the classes and methods for spatial data from package sp, and for time series data from package xts. The goal is to cover a number of useful representations for spatio-temporal sensor data, and results from predicting (spa- tial and/or temporal interpolation or smoothing), aggregating, or subsetting them, and to represent trajectories. The goals of this paper are to explore how spatio-temporal data can be sensibly represented in classes, and to find out which analysis and visualisation methods are useful and feasible. We discuss the time series convention of representing time intervals by their starting time only. This vignette is the main reference for the R package spacetime; it been published as Pebesma (2012), but is kept up-to-date with the software.

Keywords:˜Time series analysis, spatial data, spatio-temporal statistics, Geographic Informa- tion Systems.

1. Introduction

Spatio-temporal data are abundant, and easily obtained. Examples are satellite images of parts of the earth, temperature readings for a number of nearby stations, election results for voting districts and a number of consecutive elections, trajectories for people or animals possibly with additional sensor readings, disease outbreaks or volcano eruptions.

Schabenberger and Gotway (2004) argue that analysis of spatio-temporal data often happens conditionally, meaning that either first the spatial aspect is analysed, after which the temporal aspects are analysed, or reversed, but not in a joint, integral modelling approach, where space and time are not separated. As a possible reason they mention the lack of good software,

2

spacetime: Spatio-Temporal Data in R

data classes and methods to handle, import, export, display and analyse such data. This R (R Development Core Team 2011) package is a start to fill this gap.

Spatio-temporal data are often relatively abundant in either space, or time, but not in both. Satellite imagery is typically very abundant in space, giving lots of detail in high spatial resolution for large areas, but relatively sparse in time. Analysis of repeated images over time may further be hindered by difference in light conditions, errors in georeferencing resulting in spatial mismatch, and changes in obscured areas due to changed cloud coverage. On the other side, data from fixed sensors give often very detailed signals over time, allowing for elaborate modelling, but relatively little detail in space because a very limited number of sensors is available. The cost of an in situ sensor network typically depends primarily on its spatial density; the choice of the temporal resolution with which the sensors register signals may have little effect on total cost.

Although for example Botts, Percivall, Reed, and Davidson (2007) describe a number of open standards that allow the interaction with sensor data (describing sensor characteristics, requesting observed values, planning sensors, and processing raw sensed data to predefined events), the available statistical or geographic information system (GIS) software for this is in an early stage, and scattered. This paper describes an attempt to combine available infrastructure in the R statistical environment with ideas from statistical literature (Cressie and Wikle 2011) and data base literature (Guting ¨ and Schneider 2005) to a set of useful classes and methods for manipulating, plotting and analysing spatio-temporal data. A number of case studies from different application areas will illustrate its use.

The paper is structured as follows. Section˜2 describes how spatio-temporal data are usually recorded in tables. Section˜3 describes a number of useful spatio-temporal layouts. Section˜4 introduces classes and methods for data, based on these layouts. Section˜5 presents a number of useful graphs for spatio-temporal data, and implementations for these. Section˜6 discusses the spatial and temporal footprint, or support, of data, and how time intervals are dealt with in practice. Section˜7 presents a number of worked examples, some of which include statistical analysis on the spatio-temporal data. Section˜8 points to further material, including further vignettes in package spacetime on spatio-temporal overlay and aggregation, and on using proxy data sets to PostgreSQL tables when data are too large for R. Section˜9 finishes with a discussion.

This paper is also found as a vignette in package spacetime, which implements the classes and methods for spatio-temporal data described here. The vignette is kept up-to-date with the software.

2. How spatio-temporal data are recorded in tables

For reasons of simplicity, spatio-temporal data often come in the form of single tables. If this is the case, they come in one of three forms:

time-wide where different columns reflect different moments in time,

space-wide where different columns reflect different measurement locations or areas, or

long formats where each record reflects a single time and space combination.

Journal of Statistical Software

3

Alternatively, they may be stored in different, related tables, which is more typical for rela- tional data bases, or in tree structures which is typical for xml files. We will now illustrate the different single-table formats with simple examples.

2.1.

Time-wide format

 

Spatio-temporal data for which each location has data for each time can be provided in two so-called wide formats. An example where a single column refers to a single moment or period in time is found in the North Carolina Sudden Infant Death Syndrome (sids) data set (Symons, Grimson, and Yuan 1983) available from package maptools Lewin-Koh, Bivand, Pebesma, Archer, Baddeley, Bibiko, Dray, Forrest, Friendly, Giraudoux, Golicher, Rubio, Hausmann, Hufthammer, Jagger, Luque, MacQueen, Niccolai, Short, Stabler, and Turner (2011), which is in the time-wide format:

R>

library("foreign")

 

R>

read.dbf(system.file("shapes/sids.dbf",

package="maptools"))[1:5,c(5,9:14)]

 

NAME

BIR74

SID74

NWBIR74

BIR79

SID79

NWBIR79

 

1

Ashe

1091

1

10

1364

0

19

2

Alleghany

 

487

0

10

542

3

12

3

Surry

3188

 

5

208

3616

6

260

4

Currituck

 

508

1

123

830

2

145

5

Northampton

1421

 

9

1066

1606

3

1197

 

where columns refer to a particular time: SID74 contains to the infant death syndrome cases for each county at a particular time period (1974-1984).

2.2.

Space-wide format

 

The Irish wind data (Haslett and Raftery 1989) available from package gstat (Pebesma 2004),

for which the first six records and 9 of the stations (abbreviated by RPT, VAL, ... by

)

are shown

R>

data("wind",

package

=

"gstat")

 

R>

wind[1:6,1:12]

 

year

month

day

RPT

VAL

ROS

KIL

SHA

BIR

DUB

CLA

MUL

1

61

1

1

15.04

14.96

13.17

9.29

13.96

9.87

13.67

10.25

10.83

2

61

1

2

14.71

16.88

10.83

6.50

12.62

7.67

11.50

10.04

9.79

3

61

1

3

18.50

16.88

12.33

10.13

11.17

6.17

11.25

8.04

8.50

4

61

1

4

10.58

6.63

11.75

4.58

4.54

2.88

8.63

1.79

5.83

5

61

1

5

13.33

13.25

11.42

6.17

10.71

8.21

11.92

6.54

10.92

6

61

1

6

13.21

8.12

9.96

6.67

5.37

4.50

10.67

4.42

7.17

are in space-wide format: each column refers to another wind measurement location, and the rows reflect a single time period; wind was reported as daily average wind speed in knots (1 knot = 0.5418 m/s).

4

spacetime: Spatio-Temporal Data in R

2.3.

Long format

 

Finally, panel data are shown in long form, where the full spatio-temporal information is held in a single column, and other columns denote location and time. In the Produc data set (Baltagi 2001), a panel of 48 observations from 1970 to 1986 available from package plm (Croissant and Millo 2008), the first five records and nine columns are

R>

data("Produc",

package

=

"plm")

 

R>

Produc[1:5,1:9]

 

state

year

pcap

hwy

water

util

pc

gsp

emp

1

ALABAMA

1970

15032.67

7325.80

1655.68

6051.20

35793.80

28418

1010.5

2

ALABAMA

1971

15501.94

7525.94

1721.02

6254.98

37299.91

29375

1021.9

3

ALABAMA

1972

15972.41

7765.42

1764.75

6442.23

38670.30

31303

1072.3

4

ALABAMA

1973

16406.26

7907.66

1742.41

6756.19

40084.01

33430

1135.5

5

ALABAMA

1974

16762.67

8025.52

1734.85

7002.29

42057.31

33749

1169.8

where the first two columns denote space and time (the default assumption for package plm), and e.g., pcap reflects private capital stock.

None of these examples has strongly referenced spatial or temporal information: it is from the data alone not clear that the number 1970 refers to a year, or that ALABAMA refers to a state, and where this state is. Section 7 shows for each of these three cases how the data can be converted into classes with strongly referenced space and time information.

 

3. Space-time layouts

 

In the following we will use the word spatial feature (Herring 2011) to denote a spatial entity. This can be a particular spatial point (location), a line or set of lines, a polygon or set of polygons, or a pixel (grid or raster cell). For a particular feature, one or more measurements are registered at particular moments in time.

Four layouts of space-time data will be discussed next. Two of them reflect lattice layouts, one that is efficient when a particular spatial feature has data values for more than one time point, and one that is most efficient when all spatial feature have data values at each time point. Two others reflect irregular layouts, one of them specializes to trajectories.

3.1.

Spatio-temporal full grids

 

A full space-time grid of observations for spatial features (points, lines, polygons, grid cells) 1

s i ,i = 1,

n and observation time t j , j

= 1,

m is obtained when the full set of n × m nm. We choose to cycle spatial features first,

...

,

, set of observations z k is stored, with k = 1,

...

, so observation k corresponds to feature s i , i = ((k 1) % n) + 1 and with time moment t j ,

...

j = ((k 1)/n) + 1, with / integer division and % integer division remainder (modulo). The t j are assumed to be in time order.

In this data class (top left in Figure˜1), for each spatial feature, the same temporal sequence of data is sampled. Alternatively one could say that for each moment in time, the same set of

1 note that neither spatial features nor time points need to follow a regular layout

Journal of Statistical Software

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3rd

3rd

Spatial features

Spatial features

2nd

2nd

1st

1st

Spatial features

STF: full grid layout

7 10 8 11 9 12
7 10
8 11
9 12
1 4 2 5 3 6 ●
1 4
2 5
3 6
7 10 8 11 9 12 1 4 2 5 3 6 ● ● ● ●
7 10 8 11 9 12 1 4 2 5 3 6 ● ● ● ●
● ● ● ● ● ● ● ● ●
● ● ● ● ● ● ● ●
● ● ●

STS: sparse grid layout

● 4[2,2] 5[3,2] 3[3,1] ● ● ● ● 2[2,1] 1[1,1] ● ● ● ● ● ●
4[2,2]
5[3,2]
3[3,1]
2[2,1]
1[1,1]
7[2,4]
6[1,3]

1st

3rd

4th

1st

2nd

4th

Time points

Time points

STI: irregular layout

5 ● ● 3 ● ● 2 ● ● 1 4 ● ● ● ● Spatial
5
3
2
1
4
Spatial features
1st,4th
3rd
5th

STT: trajectory

Journal of Statistical Software 5 3rd 3rd Spatial features Spatial features 2nd 2nd 1st 1st Spatial
Journal of Statistical Software 5 3rd 3rd Spatial features Spatial features 2nd 2nd 1st 1st Spatial
Journal of Statistical Software 5 3rd 3rd Spatial features Spatial features 2nd 2nd 1st 1st Spatial
Journal of Statistical Software 5 3rd 3rd Spatial features Spatial features 2nd 2nd 1st 1st Spatial
Journal of Statistical Software 5 3rd 3rd Spatial features Spatial features 2nd 2nd 1st 1st Spatial
Journal of Statistical Software 5 3rd 3rd Spatial features Spatial features 2nd 2nd 1st 1st Spatial

1st

2nd

4th

Time points

Time points

Figure 1: Four space-time layouts: (i) the top-left: full grid (STF) layout stores all space-time combinations; (ii) top-right: the sparse grid (STS) layout stores only the non-missing space- time combinations on a lattice; (iii) bottom-left: the irregular (STI) layout: each observation has its spatial feature and time stamp stored, in this example, spatial feature 1 is stored twice – the fact that observations 1 and 4 have the same feature is not registered; (iv) bottom right:

simple trajectories (STT), plotted against a common time axis. It should be noted that in both gridded layouts the grid is in space-time, meaning that spatial features can be gridded, but can also be any other non-gridded type (lines, points, polygons).

6

spacetime: Spatio-Temporal Data in R

spatial entities is sampled. Unsampled combinations of (space, time) are stored in this class, but are assigned a missing value NA.

It should be stressed that for this class (and the next) the word grid in spatio-temporal grid refers to the layout in space-time, not in space. Examples of phenomena that could well be represented by this class are regular (e.g., hourly) measurements of air quality at a spatially irregular set of points (measurement stations), or yearly disease counts for a set of administrative regions. An example where space is gridded as well could be a sequence of rainfall images (e.g., monthly sums), interpolated to a spatially regular grid.

  • 3.2. Spatio-temporal sparse grids

A sparse grid has the same general layout, with measurements laid out on a space time grid (top right in Figure˜1), but instead of storing the full grid, only non-missing valued observations z k are stored. For each k, an index [i, j] is stored that refers which spatial feature i and time point j the value belongs to.

Storing data this way may be efficient

If full space-time lattices have many missing or trivial values (e.g., when one want to store features or grid cells where fires were registered, discarding those that did not),

If a limited set of spatial features each have different time instances (e.g., to record the times of crime cases for a set of administrative regions), or,

If for a limited set of times the set of spatial features varies (e.g., locations of crimes registered per year, or spatially misaligned remote sensing images).

  • 3.3. Spatio-temporal irregular data

Space-time irregular data cover the case where time and space points of measured values have no apparent organisation: for each measured value the spatial feature and time point is stored, as in the long format. This is equivalent to the (maximally) sparse grid where the index for observation k is [k, k], and hence can be dropped. For these objects, n = m equals the number of records. Spatial features and time points need not be unique, but are replicated in case they are not.

Any of the gridded types can be represented by this layout, in principle, but this would have the disadvantages that

Spatial features and time points need to be stored for each data value, and would be redundant,

The regular layout is lost, and needs be retrieved indirectly, Spatial and temporal selection would be inefficient, as the grid structure forms an index.

Examples of phenomena that are best served by this layout could be spatio-temporal point processes, such as crime or disease cases or forest fires. Other phenomena could be measure- ments from mobile sensors (when the trajectory sequence is not of importance).

Journal of Statistical Software

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3.4. Interval time, moving objects, trajectories

In their book“moving objects databases”, Guting ¨ and Schneider (2005) distinguish 10 different data types in space-time. In particular, they define for point features 2 .

a Sets of events without temporal duration (time is an instant), e.g., accidents, lightning, birth, death;

b Sets of events with a temporal duration but no movement, e.g., a tree, a (point in the) capital of a country, people’s home address;

c (Sets of) moving points, e.g., the trajectories of one or more persons, or birds.

To accomodate this typology we distinguish three cases, shown in figure 2:

(i) Time is instant and the feature is not moving (it may only exist at a time instant), (ii) Time is interval, objects do not move during this interval, (iii) Time is instant and features move (objects exist between time instants and may move) along a trajectory.

When time reflects intervals, it means that the spatial feature (spatial location or extent of the observation) or its associated data values does not change during this interval, but reflects the value or state during this interval. An examples is the yearly mean temperature of a country or of a set of locations, or the existence (duration) of a nation with a particular layout of its boundaries.

Time instants can reflect the moments of change (e.g., the start of the meteorological summer), or events with a zero or negligible duration (e.g., an earthquake, a lightning).

Movement reflects the fact that moving objects exist and may change location during a time interval. For moving object data, time instants reflect the location at a particular moment, and movement occurs between registered (time, feature) pairs, and must be continuous.

Trajectories cover the case where sets of (irregular) space-time points form sequences, and depict a trajectory. Their grouping may be simple (e.g., the trajectories of two persons on different days), nested (for several objects, a set of trajectories representing different trips) or complex (e.g., with objects that split, merge, or disappear).

Examples of trajectories can be human trajectories, mobile sensor measurements (where the sequence is kept, e.g., to derive the speed and direction of the sensor), or trajectories of tornados where the tornado extent of each time stamp can be reflected by a different polygon.

4. Classes and methods for spatio-temporal data

The different layouts, or types, of spatio-temporal data discussed in Section˜3 have been implemented in the spacetime R package, along with methods for import, export, coercion, selection, and visualisation.

2

They obtain 10 types by adding the singular/atomic form of a and b, distinguishing area from point features.

and doubling this

set

of

5

by

8

spacetime: Spatio-Temporal Data in R

time: instance time: instance, moving objects s1 s1 s2 s2 s3 s3 t1 t2 t3 t4
time: instance
time: instance, moving objects
s1
s1
s2
s2
s3
s3
t1
t2
t3
t4
t1
t2
t3
t4
time: consecutive intervals
time: arbitrary intervals
s1
s1
s2
s2
s3
s3
t1
t2
t3
t4
t1
t2
t3
t4

Figure 2: Time instant (top left), object movement (top right), time interval with consecutive (bottom left) or arbitrary (bottom right) intervals. s 1 refers to the first feature/location, t 1 to the first time instance or interval, thick lines indicate time intervals, arrows indicate movement. Filled circles denote start time, empty circles end times, intervals are right-closed.

4.1. Classes

The classes for the different layouts are shown in Figure˜3. Similar to the classes of package sp (Pebesma and Bivand 2005; Bivand, Pebesma, and Gomez-Rubio 2008), the classes all derive from a base class ST which is not meant to represent actual data. The first order derived classes specify particular spatio-temporal geometries (i.e., only the spatial and temporal information), the second order derived classes augment each of these with actual data, in the form of a data.frame.

To store temporal information, we chose to use objects of class xts in package xts (Ryan and Ulrich 2011) for time, because

It extends the functionality of package zoo (Zeileis and Grothendieck 2005),

It supports several basic types to represent time or date:

Date,

POSIXt,

timeDate,

yearmon, and yearqtr, It has good tools for aggregation over time using arbitrary aggregation functions, essen- tially deriving this from package zoo (Zeileis and Grothendieck 2005), It has a flexible syntax to select time periods that adheres to ISO 8601 3 .

An overview of the different time classes in R is found in Ripley and Hornik (2001). Further advice on which classes to use is found in Grothendieck and Petzoldt (2004), or in the CRAN task view on time series analysis.

Journal of Statistical Software

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ST sp: Spatial time: xts endTime: POSIXct STF full lattice STFDF data: data.frame STS sparse lat.
ST
sp: Spatial
time: xts
endTime: POSIXct
STF
full lattice
STFDF
data: data.frame
STS
sparse lat.
STSDF
index: matrix
data: data.frame
STI
irregular
STIDF
data: data.frame
STT
trajectory
STTDF
traj: list
data: data.frame
geometries
with data values

Figure 3: Classes for spatio-temporal data in package spacetime. Arrows denote inheritance, lower side of boxes list slot name and type, green lines indicate possible coercions (both ways).

For spatial interpolation, we used the classes deriving from Spatial in package sp (Pebesma and Bivand 2005; Bivand et˜al. 2008) because

They are the dominant set of classes in R for dealing with spatial data, They are interfaced to key external libraries through packages rgdal and rgeos, and, They provide a single interface to dealing with points, lines, polygons and grids.

We do not use xts or Spatial objects to store spatio-temporal data values, but we use data.frame to store data values. For purely temporal information the xts objects can be used, and for purely spatial information the sp objects can be used. These will be recycled appropriately when coercing to a long format data.frame.

The spatial features supported by package sp are two-dimensional for lines and polygons, but may be higher (three-) dimensional for spatial points, pixels and grids.

  • 4.2. Methods

The main methods for spatio-temporal data implemented in packages spacetime are listed in table 1. Their usage is illustrated in examples that follow.

  • 4.3. Creation

Construction of spatio-temporal objects essentially needs specification of the spatial, the tem- poral, and the data values. The documentation of stConstruct contains examples of how

10

spacetime: Spatio-Temporal Data in R

method

what it does

stConstruct

Creates STFDF or STIDF objects from single or multiple tables

[[,

$, $<-

Select or replace data values

[

Select spatial and/or temporal subsets, and/or data vari- ables

as coerce to other spatio-temporal objects, xts, Spatial,

stplot

matrix, or data.frame create spatio-temporal plots, see Section˜5

over

overlay: retrieve index or data values of one object at the

aggregate

locations and times of another aggregate data values over particular spatial, temporal, or

spatio-temporal domains

Table 1: Methods for spatio-temporal data in package spacetime.

this can be done from long, space-wide, and time-wide tables, or from shapefiles. A simple toy example for a full grid layout with three spatial points and four time instances is given below. First, the spatial object is created:

R>

sp

=

cbind(x

=

c(0,0,1),

y

=

c(0,1,1))

 

R>

row.names(sp)

 

=

paste("point",

1:nrow(sp),

sep="")

R>

library(sp)

 

R>

sp

=

SpatialPoints(sp)

 

Then, the time points are defined as four time stamps, one hour apart, starting Aug 5 2010, 10:00 GMT.

R> time = as.POSIXct("2010-08-05", tz = "GMT")+3600*(10:13)

Next, a data.frame with the data values is created:

R>

m

=

c(10,20,30)

#

means

for

each

of

the

3

point

locations

R>

values

=

rnorm(length(sp)*length(time),

 

mean

=

rep(m,

4))

R>

IDs

=

paste("ID",1:length(values),

sep

=

"_")

 

R>

mydata

=

data.frame(values

=

signif(values,

3),

ID=IDs)

And finally, the STFDF object can be created by:

R>

library(spacetime)

 

R>

stfdf

=

STFDF(sp,

time,

data

=

mydata)

In this case, as no endTime is specified, it is assumed that time reflects time instances. Altnatively, one could specify endTime, as in

R> stfdf = STFDF(sp, time, mydata, time+60)

Journal of Statistical Software

11

where the time intervals (Section˜6.1) are one minute.

When given a long table, stConstruct creates an STFDF object if all space and time combi- nations occur only once, or else an object of class STIDF, which might be coerced into other representations.

  • 4.4. Overlay and aggregation

Aggregation of data values to a coarser spatial or temporal form (e.g., to a coarser grid, aggre- gating points over administrative regions, aggregating daily data to monthly data, or aggre- gation along an irregular set of space-time points) can be done using the method aggregate. To obtain the required aggregation predicate, i.e., the grouping of observations in space-time, the method over is implemented for objects deriving from ST. Grouping can be done based on spatial, temporal, or spatio-temporal predicates. It takes care of the case whether time reflects time instances or time intervals (see section 6.1). These methods effectively provide a spatio-temporal equivalent to what is known in geographic information science as the spatial overlay.

  • 4.5. Space and time selection with [

The idea behind the [ method for classes in sp was that objects would behave as much as possible similar to matrix and data.frame. For a data.frame, a construct like a[i,j] selects row(s) i and column(s) j. For objects deriving from Spatial, rows were taken as the spatial features (points, lines, polygons, pixels) and columns as the data variables 4 .

For the spatio-temporal data classes described here, a[i,j,k] selects spatial features i, tem- poral instances j, and data variable(s) k. Unless drop=FALSE is added to such a call, selecting a single time or single feature results in an object that is no longer spatio-temporal, but either snapshot of a particular moment, or history at a particular feature (Galton 2004).

Similar to selection on spatial objects in sp and time series objects in xts, space and time indices can be defined by index or boolean vectors, but also by higher-level expressions such as spatial areas and time periods. For instance, the selection

R> air_quality[2:3, 1:10, "PM10"]

yields air quality data for the second and third spatial features, and the first 10 time instances. Higher-level spatial and temporal expressions can be used, and

R> air_quality[Germany, "2008::2009", "PM10"]

selects the PM10 measurements for the years 2008-9, lying in Germany, when Germany is a Spatial object (e.g., a SpatialPolygons) that defines Germany.

  • 4.6. Coercion to long and wide tables

Spatio-temporal data objects can be coerced to the corresponding purely spatial objects. Objects of class STFDF will be represented in time-wide form, where only the first (selected) data variable is retained:

4 a convention that was partially broken for class SpatialGridDataFrame, where a[i,j,k] could select the k-th data variable of the spatial grid selection with spatial grid row(s) i and column(s) j, unless the length of i equals the number of grid cells.

12

spacetime: Spatio-Temporal Data in R

R>

xs1

=

as(stfdf,

"Spatial")

R>

class(xs1)

 

[1]

"SpatialPointsDataFrame"

 

attr(,"package")

 

[1]

"sp"

 

R>

xs1

 

coordinates

X2010.08.05.10.00.00

X2010.08.05.11.00.00

point1

 

(0,

0)

9.66

9.64

point2

(0,

1)

21.20

19.50

point3

(1,

1)

29.90

32.10

X2010.08.05.12.00.00

X2010.08.05.13.00.00

point1

 

8.98

11.4

point2

19.60

19.8

point3

30.20

29.8

as time values are difficult to retrieve from these column names, this object gets the proper time values as an attribute:

R> attr(xs1, "time")

[1]

"2010-08-05

10:00:00

GMT"

"2010-08-05

11:00:00

GMT"

[3]

"2010-08-05

12:00:00

GMT"

"2010-08-05

13:00:00

GMT"

Objects of class STSDF or STIDF will be represented in long form, where time is added as additional column:

R>

x

=

as(stfdf,

"STIDF")

R>

xs2

=

as(x,

"Spatial")

R>

class(xs2)

 

[1]

"SpatialPointsDataFrame"

attr(,"package")

 

[1]

"sp"

 

R> xs2[1:4,]

coordinates

values

ID

time

  • 1 (0,

0)

9.66

ID_1

2010-08-05

10:00:00

  • 2 (0,

1)

21.20

ID_2

2010-08-05

10:00:00

  • 3 (1,

1)

29.90

ID_3

2010-08-05

10:00:00

  • 4 (0,

0)

9.64

ID_4

2010-08-05

11:00:00

Journal of Statistical Software

13

5. Graphs of spatio-temporal data

5.1. stplot: panels, space-time plots, animation

The stplot method can create a few specialized plot types for the classes in the spacetime package. They are:

multi-panel plots In this form, for each time step (selected) a map is plotted in a separate panel, and the strip above the panel indicates what the panel is about. The panels share x- and y-axis, no space needs to be lost by separating white space, and a common legend is used. Three types are implemented for STFDF data:

The x and y axis denote space, an example for gridded data is shown in Figure˜4, for polygon data in Figure˜9. The stplot is a wrapper around spplot in package sp, and inherits most of its options,

The x and y axis denote time and value; one panel for each spatial feature, colors may indicate different variables (mode="tp"); see Figure˜5 (left),

The x and y axis denote time and value; one panel for each variable, colors may denote different features (mode="ts"); see Figure˜5 (right).

For both cases with time is on the y-axis (Figure˜5), values over time for different variables or features are connected with lines, as is usual with time series plots. This can be changed to symbols by specifying type=’p’.

space-time plots Space-time plots show data in a space-time cross-section, with e.g., space on the x-axis and time on the y-axis. (See also Figure˜1.)

Hovm¨oller diagrams (Hovm¨oller 1949) are an example of these for full space-time lat- tices, i.e., objects of class STFDF. To obtain such a plot, the arguments mode and scaleX

should be considered; some special care is needed when only the x- or y-axis needs to

be plotted instead of the spatial index (1

n);

details are found in the stplot documen-

... tation. An example of a Hovm¨oller-style plot with station index along the x-axis and

time along the y-axis is obtained by

R>

scales=list(x=list(rot

=

45))

R>

stplot(wind.data,

mode

=

"xt",

scales

=

scales,

xlab

=

NULL)

and shown in Figure˜6. Hovm¨oller plots.

Note that the y-axis direction is opposite to that of regular

animated plots Animation is another way of displaying change over time; a sequence of spplots, one for each time step, is looped over when the parameter animate is set to a positive value (indicating the time in seconds to pause between subsequent plots).

Time series plots Time series plots are a fairly common type of plot in R. Package xts has a plot method that allows univariate time series to be plotted. Many (if not most) plot routines in R support time to be along the x- or y-axis. The plot in Figure˜7 was generated by using package lattice (Sarkar 2008), and uses a colour palette from package RColorBrewer (Neuwirth 2011).

14

spacetime: Spatio-Temporal Data in R

1961−04−14 09:20:00 1961−04−11 04:00:00 1961−04−07 22:40:00 1961−04−04 17:20:00 1961−04−01 12:00:00
1961−04−14 09:20:00
1961−04−11 04:00:00
1961−04−07 22:40:00
1961−04−04 17:20:00
1961−04−01 12:00:00
1961−04−14 09:20:00 1961−04−11 04:00:00 1961−04−07 22:40:00 1961−04−04 17:20:00 1961−04−01 12:00:00 1961−04−17 14:40:00 1961−04−24 01:20:00 1961−04−27 06:40:00
1961−04−14 09:20:00 1961−04−11 04:00:00 1961−04−07 22:40:00 1961−04−04 17:20:00 1961−04−01 12:00:00 1961−04−17 14:40:00 1961−04−24 01:20:00 1961−04−27 06:40:00
1961−04−14 09:20:00 1961−04−11 04:00:00 1961−04−07 22:40:00 1961−04−04 17:20:00 1961−04−01 12:00:00 1961−04−17 14:40:00 1961−04−24 01:20:00 1961−04−27 06:40:00
1961−04−17 14:40:00 1961−04−24 01:20:00 1961−04−27 06:40:00 1961−04−30 12:00:00 1961−04−20 20:00:00
1961−04−17 14:40:00
1961−04−17 14:40:00
1961−04−24 01:20:00 1961−04−27 06:40:00 1961−04−30 12:00:00 1961−04−20 20:00:00
1961−04−24 01:20:00
1961−04−27 06:40:00
1961−04−30 12:00:00
1961−04−20 20:00:00
14 spacetime : Spatio-Temporal Data in R 1961−04−14 09:20:00 1961−04−11 04:00:00 1961−04−07 22:40:00 1961−04−04 17:20:00 1961−04−01ISO 8601:2004 , a time stamp like 2010-05 refers to the full month of May, 2010, and so reflects a time interval . As a selection criterion, xts will include everything inside the following interval: R> library(xts) R> .parseISO8601( 2010-05 ) $first.time " id="pdf-obj-13-32" src="pdf-obj-13-32.jpg">

0.5

0.0

−0.5

−1.0

Figure 4: Space-time interpolations of wind (square root transformed, detrended) over Ireland using a separable product covariance model, for 10 time points regularly distributed over the month for which daily data was considered (April, 1961).

6. Spatial footprint or support, time intervals, moving objects

6.1. Time periods or time instances

Most data structures for time series data in R have, explicitly or implicitly, for each record a time stamp, not a time interval. The implicit assumption seems to be (i) the time stamp is a moment, (ii) this indicates either the real moment of measurement / registration, or the start of the interval over which something is aggregated (summed, averaged, maximized). For financial “Open, high, low, close” data, the “Open” and “Close” refer to the values at the moment the stock exchange opens and closes, meaning time instances, whereas “high” and “low” are aggregated values – the minimum and maximum price over the time interval between opening and closing times.

Package lubridate (Grolemund and Wickham 2011) allows one to explicitly define and com- pute with time intervals (e.g., Allen (1983)). It does not provide structures to attach these intervals to time series data. As xts does not support these times as index, spacetime does also not support it.

According to ISO 8601:2004, a time stamp like 2010-05 refers to the full month of May, 2010, and so reflects a time interval. As a selection criterion, xts will include everything inside the following interval:

R>

library(xts)

R>

.parseISO8601( 2010-05 )

$first.time

Journal of Statistical Software

15

values

values

pcap hwy util water

100000

50000

0

1970

1975

1980

1985

california arkansas arizona alabama
california arkansas arizona alabama
california arkansas arizona alabama

california

california
arkansas
arkansas
arizona
arizona
alabama
alabama

1970

1975

1980

1985

100000

50000

0

time

arizona alabama

california arkansas

100000

50000

0

1970

1975

1980

1985

pcap util water hwy
pcap util water hwy
pcap util water hwy

pcap

pcap
pcap

util

util
water
water
hwy
hwy

1970

1975

1980

1985

100000

50000

0

time

Figure 5: Time series for four variables and four features plotted with stplot, with mode="tp"

(left) and mode="ts" (right); see also Section˜7.2.

[1]

"2010-05-01

CEST"

$last.time

[1]

"2010-05-31

23:59:59

CEST"

and this syntax lets one define, unambiguously, yearly, monthly, daily, hourly or minute

intervals, but not e.g. 10- ˜ or 30-minute intervals. For a particular interval, the full specification

is needed:

R> .parseISO8601( 2010-05-01T13:30/2010-05-01T13:39 )

$first.time

 

[1]

"2010-05-01

13:30:00

CEST"

$last.time

 

[1]

"2010-05-01

13:39:59

CEST"

When matching two sequences of time (Figure˜8) in order to overlay or aggregate, it matters

whether each of the sequences reflect instances, one of them reflects time intervals and the

other instances, or both reflect time intervals. All of these cases are accommodated for.

Objects in spacetime register both (start) time and end time. By default, objects with gridded

space-time layout (Figure˜1) of class or deriving from STF or STS assume interval time, and

STI and STT objects assume instance time.

When no end times are supplied by creation and time intervals are assumed, the assumption

is that time intervals are consecutive (Figure˜2), and the last interval (for which no end time

16

spacetime: Spatio-Temporal Data in R

time

Malin Head

Belmullet

Roche's Point Valentia Roslare Kilkenny Shannon Birr

Mullingar

Clones

Claremorris

Dublin

Apr 24

Apr 17

Apr 10

Apr 03

16 spacetime : Spatio-Temporal Data in R time Malin Head Belmullet Valentia Roslare Kilkenny Shannon Birr
16 spacetime : Spatio-Temporal Data in R time Malin Head Belmullet Valentia Roslare Kilkenny Shannon Birr
16 spacetime : Spatio-Temporal Data in R time Malin Head Belmullet Valentia Roslare Kilkenny Shannon Birr
16 spacetime : Spatio-Temporal Data in R time Malin Head Belmullet Valentia Roslare Kilkenny Shannon Birr
16 spacetime : Spatio-Temporal Data in R time Malin Head Belmullet Valentia Roslare Kilkenny Shannon Birr

1.0

0.5

0.0

−0.5

−1.0

−1.5

Figure 6: Space-time (Hovm¨oller) plot of wind station data.

  • 6.2. Spatial support

All examples above work with spatial points, i.e., data having a point support. The assump-

tion of data having points support is implicit for SpatialPoints features. For polygons, the

assumption will be that values reflect aggregates (e.g., sums, or averages) over the polygon.

For gridded data, it is ambiguous whether the value at the grid cell centre is meant (e.g.,

for DEM data) or an aggregate over the grid cell (typical for remote sensing imagery). The

Spatial* objects of package sp have no explicit information about the spatial support.

7. Worked examples

This section shows how existing data in various formats can be converted into ST classes, and

how they can be analysed and/or visualised.

  • 7.1. North Carolina SIDS

As an example, the North Carolina Sudden Infant Death Syndrome (sids) data will be used.

Journal of Statistical Software

17

1.0 0.5 Roche's Valentia Point Birr Shannon Kilkenny Roslare 0.0 Claremorris Mullingar Dublin −0.5 Clones Malin
1.0
0.5
Roche's Valentia Point
Birr Shannon Kilkenny Roslare
0.0
Claremorris Mullingar Dublin
−0.5
Clones
Malin Belmullet Head
−1.0
−1.5
Apr 03
Apr 10
Apr 17
Apr 24
May 01
speed

1961

Figure 7: Time series plot of daily wind speed at 12 stations, used for interpolation in Figure˜4.

x y 1 2 3 4 object
x
y
1
2
3
4
object

time

Figure 8: Matching two time sequences, assuming x reflects time intervals, and y reflects time

instances. Note that the last interval extends the last time instance of x.

These data were first analysed by Symons et˜al. (1983), and first published and analysed

in a spatial setting by Cressie and Chan (1989). They are available from package maptools

(Lewin-Koh et˜al. 2011). The data are sparse in time (aggregated to 2 periods of unequal

length, according to the documentation in package spdep), but have polygons in space. First,

we will prepare the spatial data:

R>

library("maptools")

 

R>

fname

=

system.file("shapes/sids.shp",

package="maptools")[1]

R>

nc

=

readShapePoly(fname,

proj4string=CRS("+proj=longlat

+datum=NAD27"))

then, we construct the time sequence:

R>

time

=

as.POSIXct(c("1974-07-01",

"1979-07-01"),

tz

=

"GMT")

R>

endTime

=

as.POSIXct(c("1978-06-30",

"1984-06-30"),

tz

=

"GMT")

and we construct the data values table, in long form, by

18

spacetime: Spatio-Temporal Data in R

R>

data

=

data.frame(

 

+

BIR

=

c(nc$BIR74,

nc$BIR79),

+

NWBIR

=

c(nc$NWBIR74,

nc$NWBIR79),

+

SID

=

c(nc$SID74,

nc$SID79))

These three components are put together by function STFDF:

R>

nct

=

STFDF(sp

=

as(nc,

"SpatialPolygons"),

time,

data,

endTime)

7.2. Panel data

The panel data discussed in Section˜2 are imported as a full spatio-temporal data.frame

(STFDF), and linked to the proper state polygons of maps. We can obtain the states polygons

from package map (Brownrigg and Minka 2011) by:

R>

library("maps")

 

R>

states.m

=

map( state ,

plot=FALSE,

fill=TRUE)

R>

IDs

<-

sapply(strsplit(states.m$names,

":"),

function(x)

x[1])

R>

library("maptools")

 

R>

states

=

map2SpatialPolygons(states.m,

IDs=IDs)

we obtain the time points by:

R>

yrs

=

1970:1986

 

R>

time

=

as.POSIXct(paste(yrs,

"-01-01",

sep=""),

tz

=

"GMT")

We obtain the data table (already in long format) by

 

R>

library("plm")

 

R>

data("Produc")

When combining all this information, we do not need to reorder states because states and

Produc

order

states alphabetically.

present in Produc table (record 8):

We need to de-select District of Columbia, which is not

R>

#

deselect

District

of

Columbia,

polygon

8,

which

is

not

present

in

Produc:

R>

Produc.st

=

STFDF(states[-8],

time,

Produc[order(Produc[2],

Produc[1]),])

R>

library(RColorBrewer)

 

R>

stplot(Produc.st[,,"unemp"],

yrs,

col.regions

=

brewer.pal(9,

"YlOrRd"),cuts=9)

produces the plot shown in Figure˜9.

Time and state were not removed from the data table on construction; printing these data

after coercion to data.frame can then be used to verify that time and state were matched

correctly.

The routines in package plm can be used on the data, when back transformed to a data.frame,

when index is used to specify which variables represent space and time (the first two columns

from the data.frame no longer contain state and year). For instance, to fit a panel linear

model for gross state products (gsp) to private capital stock (pcap), public capital (pc), labor

input (emp) and unemployment rate (unemp), we get

Journal of Statistical Software

19

Journal of Statistical Software 19 Figure 9: Unemployment rate per state, over the years 1970-1986. R>

Figure 9: Unemployment rate per state, over the years 1970-1986.

R>

zz

<-

plm(log(gsp)

~

log(pcap)

+

log(pc)

+

log(emp)

+

unemp,

+

data

=

as.data.frame(Produc.st),

index

=

c("state",

"year"))

where the output of summary(zz) is left out for brevity. More details are found in Croissant

and Millo (2008) and Millo and Piras (2012).

7.3. Interpolating Irish wind

This worked example is a modified version of the analysis presented in demo(wind) of package

gstat (Pebesma 2004). This demo is rather lengthy and reproduces much of the original

analysis in Haslett and Raftery (1989). Here, we will reduce the material and focus on the

use of spatio-temporal classes.

First, we will load the wind data from package gstat. It has two tables, station locations

in a data.frame, called wind.loc, and daily mean wind speed in data.frame wind. We

now convert character representation (such as 51d56’N) to proper numerical coordinates, and

convert the station locations to a SpatialPointsDataFrame object. A plot of these data is

shown in Figure˜10.

20

spacetime: Spatio-Temporal Data in R

R>

library("gstat")

 

R>

data("wind")

R>

wind.loc$y

=

as.numeric(char2dms(as.character(wind.loc[["Latitude"]])))

R>

wind.loc$x

=

as.numeric(char2dms(as.character(wind.loc[["Longitude"]])))

R>

coordinates(wind.loc)

=

~x+y

R>

proj4string(wind.loc)

=

"+proj=longlat

+datum=WGS84"

Malin Head Belmullet Clones Claremorris Mullingar Dublin Birr Shannon Kilkenny Roslare Valentia Roche's Point 12∞W 10∞W
Malin Head
Belmullet
Clones
Claremorris
Mullingar
Dublin
Birr
Shannon
Kilkenny
Roslare
Valentia
Roche's Point
12∞W
10∞W
8∞W
6∞W
4∞W
51∞N
52∞N
53∞N
54∞N
55∞N

Figure 10: Station locations for Irish wind data.

The first thing to do with the wind speed values is to reshape these data. Unlike the North

Carolina SIDS data of section 7.1, for we have few spatial and many time points, and so the

data in data.frame wind come in space-wide form with stations time series in columns:

R> wind[1:3,]

year

month

day

RPT

VAL

ROS

KIL

SHA

BIR

DUB

CLA

MUL

  • 1 14.96

61

1

1

15.04

13.17

9.29

13.96

9.87

13.67

10.25

10.83

14.71

  • 2 16.88

61

1

2

10.83

6.50

12.62

7.67

11.50

10.04

9.79

  • 3 16.88

61

1

3

18.50

12.33

10.13

11.17

6.17

11.25

8.04

8.50

Journal of Statistical Software

21

CLO

BEL

MAL

  • 1 15.04

12.58

18.50

  • 2 13.83

9.67

17.54

  • 3 12.71

7.67

12.75

We will recode the time columns to an appropriate time data structure,

R>

wind$time

=

ISOdate(wind$year+1900,

wind$month,

wind$day)

R>

wind$jday

=

as.numeric(format(wind$time,

%j ))

and then subtract a smooth time trend of daily means (not exactly equal, but similar to the

trend removal in the original paper):

R>

stations

=

4:15

R>

windsqrt

=

sqrt(0.5148

*

as.matrix(wind[stations]))

#

knots

->

m/s

R>

Jday

=

1:366

 

R>

windsqrt

=

windsqrt

-

mean(windsqrt)

 

R>

daymeans

=

sapply(split(windsqrt,

wind$jday),

mean)

 

R>

meanwind

=

lowess(daymeans

~

Jday,

f

=

0.1)$y[wind$jday]

 

R>

velocities

=

apply(windsqrt,

2,

function(x)

{

x

-

meanwind

})

Next, we will match the wind data to its location, by connecting station names to location

coordinates, and create a spatial points object:

R>

wind.loc

=

wind.loc[match(names(wind[4:15]),

wind.loc$Code),]

R>

pts

=

coordinates(wind.loc[match(names(wind[4:15]),

wind.loc$Code),])

R>

rownames(pts)

=

wind.loc$Station

R>

pts

=

SpatialPoints(pts,

CRS("+proj=longlat

+datum=WGS84"))

Then, we project the longitude/latitude coordinates and country boundary to UTM zone

29, using spTransform in package rgdal (Keitt, Bivand, Pebesma, and Rowlingson 2011) for

coordinate transformation:

R>

library("rgdal")

 

R>

utm29

=

CRS("+proj=utm

+zone=29

+datum=WGS84")

R>

pts

=

spTransform(pts,

utm29)

And now we can construct the spatio-temporal object from the space-wide table with veloci-

ties:

R>

wind.data

=

stConstruct(velocities,

space

=

list(values

=

1:ncol(velocities)),

+

time

=

wind$time,

SpatialObj

=

pts,

interval

=

TRUE)

R>

class(wind.data)

 

[1]

"STFDF"

attr(,"package")

 

[1]

"spacetime"

22

spacetime: Spatio-Temporal Data in R

For plotting purposes, we can obtain country boundaries from package maps:

R>

library("maptools")

 

R>

m

=

map2SpatialLines(

+

map("worldHires",

xlim

=

c(-11,-5.4),

ylim

=

c(51,55.5),

plot=F))

R>

proj4string(m)

=

"+proj=longlat

+datum=WGS84"

R>

m

=

spTransform(m,

utm29)

For interpolation, we can define a grid over the area:

 

R>

grd

=

SpatialPixels(SpatialPoints(makegrid(m,

n

=

300)),

 

+

proj4string

=

proj4string(m))

 

Next, we (arbitrarily) restrict observations to those of April 1961:

R> wind.data = wind.data[, "1961-04"]

and choose 10 time points from that period to form the spatio-temporal prediction grid:

R>

n

=

10

R>

library(xts)

 

R>

tgrd

=

seq(min(index(wind.data)),

max(index(wind.data)),

length=n)

R>

pred.grd

=

STF(grd,

tgrd)

We will interpolate with a separable exponential covariance model, with ranges 750 km and

1.5 days:

R>

v

=

list(space

=

vgm(0.6,

"Exp",

750000),

time

=

vgm(1,

"Exp",

1.5

*

3600

*

24))

R>

pred

=

krigeST(values

~

1,

wind.data,

pred.grd,

v)

R>

wind.ST

=

STFDF(grd,

tgrd,

data.frame(sqrt_speed

=

pred))

then creates the STFDF object with interpolated values, the results of which are shown in

Figure˜4, created by

R>

layout

=

list(list("sp.lines",

m,

col= grey ),

+

list("sp.points",

pts,

first=F,

cex=.5))

R>

stplot(wind.ST,

col.regions=brewer.pal(11,

"RdBu")[-c(10,11)],

+

at=seq(-1.375,1,by=.25),

 

+

par.strip.text

=

list(cex=.7),

sp.layout

=

layout)

7.4. Calculation of EOFs

Empirical orthogonal functions from STFDF objects can be computed in spatial form (default),

e.g., from data values

R> eof.data = EOF(wind.data)

or alternatively from modelled, or interpolated values:

Journal of Statistical Software

23

R> eof.int = EOF(wind.ST)

By default, spatial EOFs are competed; alternatively they can be obtained in temporal form:

R> eof.xts = EOF(wind.ST, "temporal")

the resulting object is of the appropriate subclass of Spatial in the spatial form, or of class xts

in the temporal form. Figure˜11 shows the 10 spatial EOFs obtained from the interpolated

wind data of Figure˜4.

EOF1 EOF2 EOF3 EOF4 EOF5 EOF6 EOF7 EOF8 EOF9 EOF10
EOF1
EOF2
EOF3
EOF4
EOF5
EOF6
EOF7
EOF8
EOF9
EOF10

Figure 11: EOFs of space-time interpolations of wind over Ireland (for spatial reference, see

Figure˜4), for the 10 time points at which daily data was chosen above (April, 1961).

7.5. Trajectory data: ltraj in package adehabitatLT

Trajectory objects of class ltraj in package adehabitatLT (Calenge, Dray, and Royer-Carenzi

2008) are lists of bursts, sets of sequential, connected space-time points at which an object is

registered. An example ltraj data set is obtained by 5 :

R>

library("adehabitatLT")

 

R>

data("puechabonsp")

 

R>

locs

 

=

puechabonsp$relocs

 

R>

xy

=

coordinates(locs)

 

R>

da

=

as.character(locs$Date)

 

R>

da

=

as.POSIXct(strptime(as.character(locs$Date),"%y%m%d",

tz

=

"GMT"))

R>

ltr

=

as.ltraj(xy,

da,

id

=

locs$Name)

5 taken from adehabitatLT, demo(mangltraj)

24

spacetime: Spatio-Temporal Data in R

R>

foo

=

function(dt)

dt

>

100*3600*24

 

R>

l2

=

cutltraj(ltr,

"foo(dt)",

nextr

=

TRUE)

and these data, converted to STTDF can be plotted, as panels by time and id by

R>

sttdf

=

as(l2,

"STTDF")

R>

stplot(sttdf,

by="time*id")

which is shown in Figure˜12.

time Jean time Jean time Jean time Jean time Jean time time Calou time Calou time
time Jean time Jean time Jean time Jean time Jean time time Calou time Calou time
time Jean time Jean time Jean time Jean time Jean time time Calou time Calou time
time Jean time Jean time Jean time Jean time Jean time time Calou time Calou time
time Jean time Jean time Jean time Jean time Jean time time Calou time Calou time
time Jean time Jean time Jean time Jean time Jean time time Calou time Calou time
time Jean time Jean time Jean time Jean time Jean time time Calou time Calou time
time Jean time Jean time Jean time Jean time Jean time time Calou time Calou time
time
Jean
time
Jean
time
Jean
time
Jean
time
Jean
time
time
Calou
time
Calou
time
Calou
time
Calou
time Jean time Jean time Jean time Jean time Jean time time Calou time Calou time
time Jean time Jean time Jean time Jean time Jean time time Calou time Calou time
time Brock time Brock time Brock Brock time Brock time
time
Brock
time
Brock
time
Brock
Brock
time
Brock
time
Chou Calou time Chou time Chou time Chou time
Chou
Calou
time
Chou
time
Chou
time
Chou
time

Figure 12: Trajectories, split by id (rows) and by time (columns).

7.6. Country shapes in cshapes

The cshapes (Weidmann, Kuse, and Gleditsch 2010) package contains a GIS dataset of country

boundaries (1946-2008), and includes functions for data extraction and the computation of

distance matrices. The data set consist of a SpatialPolygonsDataFrame, with the following

data variables:

Journal of Statistical Software

25

R>

library("cshapes")

 

R>

cs

=

cshp()

R>

names(cs)

 

[1]

"CNTRY_NAME"

"AREA"

"CAPNAME"

"CAPLONG"

"CAPLAT"

[6]

"FEATUREID"

"COWCODE"

"COWSYEAR"

"COWSMONTH" "COWSDAY"

[11]

"COWEYEAR"

"COWEMONTH"

"COWEDAY"

"GWCODE"

"GWSYEAR"

[16]

"GWSMONTH"

"GWSDAY"

"GWEYEAR"

"GWEMONTH"

"GWEDAY"

[21]

"ISONAME"

"ISO1NUM"

"ISO1AL2"

"ISO1AL3"

R> row.names(cs) = paste(as.character(cs$CNTRY_NAME), 1:244)

where two data bases are used, “COW” (correlates of war project 6 ) and “GW” Gleditsch and

Ward (1999). The variables COWSMONTH and COWEMONTH denote the start month

and end month, respectively, according to the COW data base.

In the following fragment, we create the time index:

R>

begin

=

as.POSIXct(paste(cs$COWSYEAR,

cs$COWSMONTH,

cs$COWSDAY,

sep="-"),

+

tz

=

"GMT")

R>

end

=

as.POSIXct(paste(cs$COWEYEAR,

cs$COWEMONTH,cs$COWEDAY,

sep="-"),

+

tz

=

"GMT")

and the spatio-temporal object:

R>

st

=

STIDF(geometry(cs),

begin,

as.data.frame(cs),

end)

A possible query would be which countries are found at 7 East and 52 North,

R>

pt

=

SpatialPoints(cbind(7,

52),

CRS(proj4string(cs)))

 

R>

as.data.frame(st[pt,,1:5])

V1

V2

sp.ID

time

  • 1 Germany

9.41437

50.57623

Federal

Republic

188

1955-05-05

  • 2 10.38084

51.09070

Germany

187

1990-10-03

 

endTime

timeIndex

CNTRY_NAME

AREA

CAPNAME

  • 1 Germany

1990-10-02

188

Federal

Republic

247366.4

Bonn

  • 2 2008-06-30

187

Germany

356448.2

Berlin

 

CAPLONG

CAPLAT

  • 1 7.1

50.73333

 
  • 2 13.4

52.51667

which turns out to be the Germany Federal Republic and Germany, that is, before and after

the merge. No data before 1955-5-5 is available.

6 Correlates

of

War

Project.

2008.

State

System

Membership

List,

v2008.1.

Online,

26

spacetime: Spatio-Temporal Data in R

8. Further material

Searching past email discussion threads on the r-sig-geo (R Special Interest Group on using

GEOgraphical data and Mapping) email list may be a good way to look for further material,

before one considers posting questions. Search strings, e.g., on the google search engine may

look like:

spacetime site:stat.ethz.ch

where the search keywords should be made more precise.

The excellent book Statistics for spatio-temporal data (Cressie and Wikle 2011) provides a

large number of methods for the analysis of mainly geostatistical data. A demo script, which

can be run by

R>

library(spacetime)

R>

demo(CressieWikle)

downloads the data from the book web site, and reproduces a number of graphs shown in the

book. It should be noted that the the book examples only deal with STFDF objects.

Section˜7.3 contains an example of a spatial interpolation with a spatio-temporal separable or